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//
// Extension.cpp
//
//
// Created by Pierre Peterlongo on 22/10/2012
//
#ifndef ASSERTS
#define NDEBUG // disable asserts, they're computationnally intensive
#endif
#include "Extension.h"
extern Bloom * bloo1;
extern BinaryBank * SolidKmers;
extern char * prefix_trashable;
Extension::Extension(const char * kmer){
// printf("CREATE EXTENSION for %s (direction:%s)\n", kmer,LeftorRight );
starting_kmer = kmer;
node_id=-1;
}
void Extension::perform_extension(const string prefix, int max_graph_depth, const char extension_type, int max_nodes, parcours_t search_mode){
terminator->reset(); // distinct extensions may share kmers, however, a unique extension doesn't.
if(extension_type==1 || extension_type==2)
IterativeExtensions::when_to_stop_extending = IterativeExtensions::After_first_contig; // sequence
else
IterativeExtensions::when_to_stop_extending = IterativeExtensions::Until_max_depth; //graph
if(extension_type==1 || extension_type==3)
IterativeExtensions::traversal_type = IterativeExtensions::SimplePaths; // strict
else
IterativeExtensions::traversal_type = IterativeExtensions::Monument; // contigs
string linear_seq_name = prefix_trashable+starting_kmer;
// construct and store the linear seqs'
IterativeExtensions::dont_output_first_nucleotide = true;
IterativeExtensions::construct_linear_seqs(starting_kmer,string(), max_graph_depth, linear_seq_name, 1, max_nodes, search_mode);
}
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